In about 1560 he started upon his major work, the Survey of London. His antiquarian interests attracted suspicion from the ecclesiastical authorities as a person "with many dangerous and superstitious books in his possession", and in February 1569 his house was searched. An inventory was made of all the books at his home, especially those "in defence of papistry", but he was able to satisfy his interrogators as to the soundness of his Protestantism.[2] A second attempt to incriminate him was made in 1570 also without success.

Stow made keen acquaintance of the leading antiquarians of his time, including William Camden, before in 1561 producing his first work, The woorkes of Geffrey Chaucer, newly printed with divers additions whiche were never in printe before. This was followed in 1565 by his Summarie of Englyshe Chronicles which was reprinted several times, with slight variations, during his lifetime. Grenville's Library is believed to have had a first-edition of Stow's Summarie and the British Library holds copies of his editions of 1567, 1573, 1590, 1598 and 1604. Stow's 1567 edition makes mention in its frontispiece of a rival publication by Richard Grafton, a dispute which later magnified.

In 1580, Stow published his Annales, or a Generale Chronicle of England from Brute until the present yeare of Christ 1580; reprinted in 1592, 1601 and 1605,[3] the last being continued to 26 March 1605, or within ten days of his death. Editions "amended" by Edmund Howes appeared in 1615 and 1631.

Under ArchbishopMatthew Parker's patronage, Stow was persuaded to produce a version of Flores historiarum by "Matthew of Westminster" published in 1567, then the Chronicle of Matthew Paris in 1571, and the Historia brevis of Thomas Walsingham in 1574. In the Chronicle of England 1590 Stow writes: "To The Honorable Sir John Hart, Lord Maior. The Chronicle written before that nothing is perfect the first time, and that it is incident to mankinde to erre and slip sometimes, but the point of fanta[s]tical fooles to preserve and continue in their errors."

At the request of Archbishop Parker he compiled a "farre larger volume", a history of Britain, but circumstances were unfavourable to its publication and the manuscript was lost.[4] Additions to the previously published works of Chaucer were twice made through Stow's "own painful labours" in the edition of 1561, referred to above, and also in 1597. A number of Stow's manuscripts are in the Harley Collection in the British Library. Some are in Lambeth Palace Library (MS 306), and were published in 1880 by the Camden Society, edited by James Gairdner, as Three Fifteenth Century Chronicles, with Historical Memoranda by John Stowe the Antiquary, and Contemporary Notes of Occurrences written by him.

The work for which Stow is best known is his Survey of London (original spelling: A Survay of London), published in 1598, which is of unique value for its detailed account of the buildings, social conditions and customs of London in the time of Queen Elizabeth I. He published a second revised edition in 1603. Following his death, a third edition, with additions by Anthony Munday appeared in 1618; a fourth by Munday and Humfrey Dyson in 1633; a fifth with interpolated amendments by John Strype in 1720; and a sixth by the same editor in 1754. The edition of 1598 was reprinted, edited by William John Thoms, in 1842, in 1846, and (with illustrations) in 1876. An edition based on that of 1598, edited by Henry Morley, was published in 1889, and has been reprinted on several occasions since.

A critical edition, based on that of 1603 and edited in two volumes by C. L. Kingsford, was published in 1908, and republished with additional notes in 1927. This remains the standard scholarly edition. A more popular single-volume edition was published in Everyman's Library, with an introduction by H. B. Wheatley, in 1912 (revised edition 1956), and has been frequently reprinted.

Stow's literary efforts did not prove very remunerative, but he accepted his relative poverty with cheerful spirit: Ben Jonson relates once walking with him when Stow jocularly asked two mendicant cripples "what they would have to take him to their order". From 1579 he was in receipt of a pension of £4 per annum from the Merchant Taylors' Company; and in 1590 he petitioned the Court of Aldermen for admission to the Freedom of the City of London, in order to reduce his expenses.[5] In about the 1590s, William Camden commissioned Stow to transcribe six autograph notebooks of John Leland in exchange for a life annuity of £8: this was probably (in part) a charitable gesture towards an old but impoverished friend.[6] In March 1604 King James I authorised Stow and his associates to collect "amongst our loving subjects their voluntary contributions and 'kind gratuities'", and himself began "the largesse for the example of others". Whilst such royal approval was welcome it reaped dividend too slowly for Stow to enjoy any substantial benefit during his lifetime.

Stow's widow commissioned a mural monument to him in the church, made of Derbyshire marble and alabaster. The work has been tentatively attributed to Nicholas Johnson.[5][8][9][10][11] It includes an effigy of Stow, which was originally coloured: he is represented seated at a desk, writing in a book (probably the revision of his Annals, which he brought down to only ten days before his death), and flanked by other books. Above him is the motto, based on a phrase of Pliny the Younger, Aut scribenda agere, aut legenda scribere ("[Blessed is he to whom it is given] either to do things that are worth writing about, or to write things that are worth reading about"). The figure holds a real quill pen, in a manner similar to the effigy of William Shakespeare at Stratford-upon-Avon: the latter monument has been attributed, on equally tentative grounds, to Nicholas Johnson's brother, Gerard.[12]

In acknowledgement of Stow's continuing reputation as the founding father of London history, the quill held by his effigy has been periodically renewed. The renewal is mentioned as taking place "annually" in 1828;[13] and, although the custom may later have fallen into abeyance, it was revived following the monument's restoration by the Merchant Taylors' Company in 1905. In 1924, the ceremony was incorporated into a special church service, with an address by a London historian; and this service continued to be held annually every April until 1991, including the years of the Second World War.[14][15][16] No services could be held in 1992 or 1993 because of damage to the church caused by the Baltic Exchange bomb of 1992. The service was revived in 1994, but since 1996 has been held only once every three years.[17] The services are jointly sponsored by the Merchant Taylors' Company and the London & Middlesex Archaeological Society, and the quill supplied by the London & Middlesex Archaeological Society. The exchange of the quill is undertaken by the Lord Mayor of London or the Master Merchant Taylor alternately.[18]

Collinson, Patrick (2001). "John Stow and nostalgic antiquarianism". In Merritt, J. F. Imagining Early Modern London: perceptions and portrayals of the city from Stow to Strype, 1598–1720. Cambridge: Cambridge University Press. pp. 27–51. ISBN0521773466.

Gadd, Ian; Gillespie, Alexandra, eds. (2004). John Stow (1525–1605) and the making of the English past: studies in early modern culture and the history of the book. London: British Library. ISBN0-7123-4864-6.

Rubinstein, Stanley (1968). "John Stow". Historians of London: an account of the many surveys, histories, perambulations, maps and engravings made about the city and its environs, and of the dedicated Londoners who made them. London: Peter Owen.